Exploring the spatiotemporal genetic heterogeneity in metastatic lung adenocarcinoma using a nuclei flow-sorting approach

Thomas Lorber, Noemi Andor, Tanja Dietsche, Valeria Perrina, Darius Juskevicius, Karen Pereira, Stephanie U. Greer, Arthur Krause, David C. Müller, Spasenija Savic Prince, Didier Lardinois, Michael Barrett, Christian Ruiz, Lukas Bubendorf

Research output: Contribution to journalArticle

1 Citation (Scopus)

Abstract

Variable tumor cellularity can limit sensitivity and precision in comparative genomics because differences in tumor content can result in misclassifying truncal mutations as region-specific private mutations in stroma-rich regions, especially when studying tissue specimens of mediocre tumor cellularity such as lung adenocarcinomas (LUADs). To address this issue, we refined a nuclei flow-sorting approach by sorting nuclei based on ploidy and the LUAD lineage marker thyroid transcription factor 1 and applied this method to investigate genome-wide somatic copy number aberrations (SCNAs) and mutations of 409 cancer genes in 39 tumor populations obtained from 16 primary tumors and 21 matched metastases. This approach increased the mean tumor purity from 54% (range 7–89%) of unsorted material to 92% (range 79–99%) after sorting. Despite this rise in tumor purity, we detected limited genetic heterogeneity between primary tumors and their metastases. In fact, 88% of SCNAs and 80% of mutations were propagated from primary tumors to metastases and low allele frequency mutations accounted for much of the mutational heterogeneity. Even though the presence of SCNAs indicated a history of chromosomal instability (CIN) in all tumors, metastases did not have more SCNAs than primary tumors. Moreover, tumors with biallelic TP53 or ATM mutations had high numbers of SCNAs, yet they were associated with a low interlesional genetic heterogeneity. The results of our study thus provide evidence that most macroevolutionary events occur in primary tumors before metastatic dissemination and advocate for a limited degree of CIN over time and space in this cohort of LUADs. Sampling of primary tumors thus may suffice to detect most mutations and SCNAs. In addition, metastases but not primary tumors had seeded additional metastases in three of four patients; this provides a genomic rational for surgical treatment of such oligometastatic LUADs.

Original languageEnglish (US)
JournalJournal of Pathology
DOIs
StateAccepted/In press - Jan 1 2019

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Genetic Heterogeneity
Neoplasms
Mutation
Neoplasm Metastasis
Chromosomal Instability
Adenocarcinoma of lung
Ploidies
Neoplasm Genes
Genomics
Gene Frequency

Keywords

  • comparative genomics
  • flow sorting
  • intratumoral heterogeneity
  • lung cancer
  • metastatic tumor evolution

ASJC Scopus subject areas

  • Pathology and Forensic Medicine

Cite this

Lorber, T., Andor, N., Dietsche, T., Perrina, V., Juskevicius, D., Pereira, K., ... Bubendorf, L. (Accepted/In press). Exploring the spatiotemporal genetic heterogeneity in metastatic lung adenocarcinoma using a nuclei flow-sorting approach. Journal of Pathology. https://doi.org/10.1002/path.5183

Exploring the spatiotemporal genetic heterogeneity in metastatic lung adenocarcinoma using a nuclei flow-sorting approach. / Lorber, Thomas; Andor, Noemi; Dietsche, Tanja; Perrina, Valeria; Juskevicius, Darius; Pereira, Karen; Greer, Stephanie U.; Krause, Arthur; Müller, David C.; Savic Prince, Spasenija; Lardinois, Didier; Barrett, Michael; Ruiz, Christian; Bubendorf, Lukas.

In: Journal of Pathology, 01.01.2019.

Research output: Contribution to journalArticle

Lorber, T, Andor, N, Dietsche, T, Perrina, V, Juskevicius, D, Pereira, K, Greer, SU, Krause, A, Müller, DC, Savic Prince, S, Lardinois, D, Barrett, M, Ruiz, C & Bubendorf, L 2019, 'Exploring the spatiotemporal genetic heterogeneity in metastatic lung adenocarcinoma using a nuclei flow-sorting approach', Journal of Pathology. https://doi.org/10.1002/path.5183
Lorber, Thomas ; Andor, Noemi ; Dietsche, Tanja ; Perrina, Valeria ; Juskevicius, Darius ; Pereira, Karen ; Greer, Stephanie U. ; Krause, Arthur ; Müller, David C. ; Savic Prince, Spasenija ; Lardinois, Didier ; Barrett, Michael ; Ruiz, Christian ; Bubendorf, Lukas. / Exploring the spatiotemporal genetic heterogeneity in metastatic lung adenocarcinoma using a nuclei flow-sorting approach. In: Journal of Pathology. 2019.
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abstract = "Variable tumor cellularity can limit sensitivity and precision in comparative genomics because differences in tumor content can result in misclassifying truncal mutations as region-specific private mutations in stroma-rich regions, especially when studying tissue specimens of mediocre tumor cellularity such as lung adenocarcinomas (LUADs). To address this issue, we refined a nuclei flow-sorting approach by sorting nuclei based on ploidy and the LUAD lineage marker thyroid transcription factor 1 and applied this method to investigate genome-wide somatic copy number aberrations (SCNAs) and mutations of 409 cancer genes in 39 tumor populations obtained from 16 primary tumors and 21 matched metastases. This approach increased the mean tumor purity from 54{\%} (range 7–89{\%}) of unsorted material to 92{\%} (range 79–99{\%}) after sorting. Despite this rise in tumor purity, we detected limited genetic heterogeneity between primary tumors and their metastases. In fact, 88{\%} of SCNAs and 80{\%} of mutations were propagated from primary tumors to metastases and low allele frequency mutations accounted for much of the mutational heterogeneity. Even though the presence of SCNAs indicated a history of chromosomal instability (CIN) in all tumors, metastases did not have more SCNAs than primary tumors. Moreover, tumors with biallelic TP53 or ATM mutations had high numbers of SCNAs, yet they were associated with a low interlesional genetic heterogeneity. The results of our study thus provide evidence that most macroevolutionary events occur in primary tumors before metastatic dissemination and advocate for a limited degree of CIN over time and space in this cohort of LUADs. Sampling of primary tumors thus may suffice to detect most mutations and SCNAs. In addition, metastases but not primary tumors had seeded additional metastases in three of four patients; this provides a genomic rational for surgical treatment of such oligometastatic LUADs.",
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